Metal Gear Solid: Chasing Phantoms
by ReversedFortune
Summary: After the discovery of the vocal cord parasite by a weapons manufacturer, Venom Snake and his Diamond Dogs must once again stop the world from plunging itself into WW3 and becoming a world ruled by silence.
1. Chapter 1

**Disclaimer:** The Metal Gear Solid franchise belongs to Hideo Kojima.

 **A/N:** Just to clear up the timeline, this takes place after "A Quiet Exit" but before the true ending, so **some spoilers** if you haven't reached that point yet. Non-edited, so I happily take credit for any mistakes, if you notice any please let me know.

Chapter 1: Step by Step

 _I am Quiet. I am, the absence of words._

 _Two weeks later…_

"Boss, your target is located in Qarya Sakhra EE village." Miller said over his radio "The cut-off that contacted us said that the man was offering some useful information in exchange for his safety."

Snake watched though his binoculars as several soviet soldiers patrolled the mass of buildings protruding from rocky ledges. Beside him, DD sat patiently, gray ears twitching hack and forth on alert.

"Apparently he was a high class weapons dealer for the soviets, but recently decided to add to his clients and started selling to the mujahidin on the side."

He couldn't help the small noise of disgust that escaped him.

"Smart, I know." Miller continued "Obviously, the soviets didn't like his new business plan when they caught wind of it, and are transporting him to the Yakho Oobo outpost later tonight for interrogation. Extract the target before the transport gets there, and its mission complete. Good luck Boss."

Putting his binoculars away, Snake reached over and scratched behind DD's ear.

"Ready boy?"

The dog gave a bark in assent, and they slowly began their descent toward the village, using boulders and large bushes as coverage from the few roaming spotlights, eventually reaching the first of many buildings that littered the area.

DD growled softly as they approached, letting him know that someone was inside. Creeping along the side, he snuck a glance through the window to spot a lone soiled huddle over what looked to be a broken radio at one of the small tables.

Silently, he pushed the metal door open, the soft groan of its hinges going unnoticed as he snuck up behind the unlucky solider. Grappling him from behind, Snake used one arm to immobilize the soviet, while the other brought a knife to his throat.

"Start talking" he commanded, putting slightly more pressure on the knife, "Where is the prisoner you're holding?"

"H…He's in that building, over there." The soldier swallowed roughly, pointing outside the window to a building which sported a communications tower on top.

"That's all I know, I swear."

Without another word, Snake put the man into a chokehold, cutting off his oxygen supply and leaving him unconscious after only a short struggle. Wood creaked underneath his weight as he made his way back outside, down a set of stairs, and to the cover of another building, DD hot on his heels.

The chatter of a small group reached his ears, and he crouched before looking around the corner. Three soviet soldiers armed with shields and helmets in addition to their usual gear were loitering around a burning trashcan, taking a break from patrol. Beyond them sat the entrance to the building where his target was located.

Snake readied his tranquilizer before lowering himself to his stomach.

"Stay" he ordered DD, and slowly began to crawl along the vey outskirts of the group until he was opposite from where he'd started. Setting himself into position, he sat up into a crouch, aimed, and fired. The first shot was a direct hit, putting one of the soldiers to sleep almost instantly, the other two gasping in shock when then man collapsed to the ground.

"Keep'em busy." Snake called

DD burst from his hiding place and charged at one of the men, sinking his teeth into his forearm with a growl. Before the remaining man had time to ready his weapon, Snake charged from behind, managing to spin him around and disarm him with a few quick strikes, before tossing him to the ground. He followed through, and soon the other solider lay on the floor stunned, the air knocked from his lungs.

"Good boy, DD." He petted the dog, who welcomed the praise with a soft yip and wagging tail. Glancing around, he settled for dragging the bodies behind a rocky alcove in order to hide them before continuing toward his target.

"Someone…help me…please…"

Approaching the building, Snake could just make out the pleas of someone being held prisoner inside.

"Boss!" Miller's voice once again came over the radio, "Intel just spotted the suspected transport vehicle in route to your position. You need to extract the target and get out of there ASAP."

"Right" Snake responded.

There was no sign from DD that any other soldiers were nearby, so he opened the door and entered the building. Withering on the ground was a middle aged man with a shaved head, dressed in a dirty blue jumpsuit, arms tied behind his back. Quickly, snake cut the ties and hoisted the man over his shoulders.

"Oh god, Thank you. I thought they were going to kill me." The man gasped.

Snake only gave an irritated grunt in response, but the man seemed to the message and silenced himself.

Using the same route they'd used to infiltrate the area, Snake and DD slowly made their way thought the buildings with the extra passenger. Luckily, no one had seemed to have noticed their missing comrades and they slipped out of the village and into the night without incident.

Snake made sure to clear the village area before securing the man in a Fulton and watching as he was lifted into the sky.

"Extraction Complete, target is confirmed on board. Excellent work Boss. Go ahead and call the chopper or exfiltrate on land."

The iDroid beeped as he designated a land zone, and minutes later, he and DD climbed aboard Pequod and watched out the window as they slowly ascended into the air.

"Departing" the pilot confirmed, and Snake slid the door of the chopper closed.

"Where to Boss?" the pilot called back Snake settled into his seat.

DD let out a large yawn before lying down, golden eye watching him intently. Well, that settled it then.

"Back to base, Pequod. We're done for today." Snake said.

"Roger that, returning to Mother Base." the pilot confirmed as the chopper banked slightly left, then leveled out.

The ride back to mother base was silent, and he made it a point to not think too deeply about that.

Just like normal, a small squad met him on the landing platform and they saluted him as he made his way past and to one of the portable showers. The cool water was a welcome relief after the extended amount of missions he completed in Afghanistan, and he emerged feeling refreshed, if not still tired.

As had become routine over the last two weeks, Snake made his way up the command platform to his quarters with DD trailing close behind, boots clanking heavily as he acknowledged the soldiers he passed with a small nod. Pushing through the door, he stepped into room and fell onto the bed with a sigh. DD squeezed himself into the space underneath as Snake pulled out his iDroid from his pocket and put in his headphones, attempting to relax as it cycled through various songs, but it wasn't until a soft, comforting humming reached his ears that sleep finally took him.

Sunlight streaming in through the window woke him. Groaning, he stretched-hearing several things pop in response-and glanced around. In the corner, DD was chewing happily on a bone, having apparently been awake long enough to go in search of breakfast. The dog glanced up, barked once happily in acknowledgement, and then went back eating. Snake let the dog be, climbing downstairs and making his way toward the common area for some early morning target practice.

"Morning Boss!" a soldier passing on guard duty called, as did several others who were passing by. Some asked him to train, and before he knew it a small group had gathered to practice CQC techniques. He hardly minded though, it was good training and better for morale if the men saw him being involved, plus it kept his mind off other things.

"Hey Boss," Miller's voice came through his iDroid just as the group was finally beginning to disperse "Ocelot says he got some interesting information from that arms dealer, something about a meeting between some higher-ups, I'll keep you posted with the details. In the meantime, a few more contracts have popped up, take a look at them when you get the chance. We're almost there Boss, step by step Diamond Dogs is growing to be bigger and better than it ever was before, pretty soon we'll be able to take down Cipher, permanently."

"Oh," he continued after a moment, reluctance coloring his tone, "by the way, I got a message from the old man. He wants to see you on the medical platform."


	2. Chapter 2: Gratitude

**Disclaimer:** The Metal Gear Solid franchise belongs to Hideo Kojima.

 **A/N:** Huge thanks to everyone who reviewed/favorited/followed the first chapter, you guys are awesome. Once again **some spoilers** if you haven't beaten the mission "A Quiet Exit".

This one is a little short, but I wanted to get it out before midterms started.

Chapter 2: Gratitude

" _I did not choose to be Quiet. I wanted to express my feelings to you. If only we shared a common tongue."_

The first thing to greet Snake as he entered the research lab was a strange mixture of antiseptic and smoke.

The room itself sported white paint, fluorescent lights, and a linoleum floor. Cabinets filled with expensive looking equipment lined the upper half of the walls while tables were placed at regular intervals around the room. The far wall was the only exception, instead boasting several computers and a large bookshelf shoved to one corner.

It was there he saw Code Talker flipping through a particularly thick volume as white smoke rose from his pipe.

"Boss, you're here. Good." Code Talker said, looking up from his book as Snake made his way across the room.

"Miller said you found something?" Snake questioned

"Perhaps." the Navajo said, snapping his book shut before replacing it on the shelf and wheeling himself over to one of the computers, Snake following close behind. A few clicks caused several graphs pop up on the screen. They appeared to detail the life cycle of several different strains of vocal cord parasites

"I have been looking into what we discussed. Normally, larva will find their way to the lungs after activation of the mating pair. This leads to the lungs being damaged and eventually the death of the host, as you already know." After a brief pull from his pipe Code Talker continued, "Using samples and data gathered from the first two outbreaks, I have been able to compare infection rates between healthy and damaged lung tissue."

The old man brought up another set of graphs.

"In general, healthy tissue has the ability to support a relatively large amount of parasitic larva before symptoms even begin to appear. The number of parasites supported by damaged lung tissue on the other hand, is severely reduced due to lack of available nutrients."

"So someone like Quiet, whose lungs are burnt…" Snake trailed off, leaving the unasked question in the air.

Code Talker nodded, seemingly pleased that he was following along.

"With how badly her lungs are burnt, it would be almost impossible for any larva to survive. Combine this with the fact that she breathes through her skin and she is at almost no risk of dying from the parasite herself."

Snake felt a wave of relief wash over him. He had hoped she would be alright, but to hear it confirmed removed a large weight from his shoulders. The thought of her dying alone in the desert of Afghanistan had filled him with an almost overwhelming sense of sadness and guilt. His relief was short-lived, however.

"That does not mean she is not dangerous." Code Talker informed him.

"What do you mean?" Snake asked

"Even though she may not feel its effects she is still a carrier. The mating pair is active, the offspring present simply die from lack of proper nutrients before they reach maturity." The Navajo explained "Given the opportunity they could spread just as quickly and easily as any other strain. But, assuming she does not interact with others, the parasite should remain isolated."

"Is there any way to stop it?"

"That is why I asked to speak with you. While studying her medical files I came across something very interesting." Code Talker motioned to several files that lay open on the desk "You know that Quiet carries a mutated strain of "the one that covers"? That it was specifically designed by Skull Face to help her heal and gives her the abilities she now possesses?"

Snake nodded "What about it?"

"Based on her situation I believed that the Wolbachia could be used to stop the vocal parasite from further larva production, as it normally would. The only complication that I could foresee was how it would affect the other parasites present in her body. Because of this, I decided to the best way to observe what would happen would be to introduce a sample of Quiets mutated strand to the Wolbachia and see how they would react to each other."

"What happened?" Snake questioned, dreading the answer that might come. It would be just his luck that the universe would be cruel. That she would be alive, breathing, but forced into a life of solitude because she had saved him.

"The Wolbachia were mutated. I am unsure how or why, but various scans have confirmed a change in their genetic makeup. Thankfully, it seems that its ability to infect and change the vocal cord parasite has remained unaffected."

"So the Wolbachia will cure her?" Snake asked

"There is always a risk, and I would prefer to gather more data, but yes." Code Talker said "There is no reason why the Wolbachia should not work as before, even in Quiet's case."

Snake sighed "Now all that's left is actually finding her."

"The Dine is resourceful" Code talker admitted, "but I doubt that she would stray too far, especially when she did not willingly leave."

"What makes you say that?"

"You would know the answer better than I." Code Talker said, "In any case, we now know the treatment will help her, which is good news. I will continue to study the mutated strains, perhaps I can learn more about how "the one that covers" managed to affect the Wolbachia in such a way."

"Right." Snake nodded his assent "Thank you."

Snake was sincerely grateful to the man. Not only had he saved the lives of countless Diamond Dogs by providing a treatment for the parasite during the first outbreak, he had proved to be an invaluable source of information, and had now just given Snake a renewed sense of hope and determination.

"Of course child, think nothing of it." The old man gave him a small smiled, looking more like an elderly grandfather than the parasitic expert that he was.

Snake left the laboratory, his shoulders lighter and mind focused. He would tell Ocelot to have the Intel team widen their search area and to send out a few more scouting party. They would find her.


End file.
